Most likely your Inventory Scans are configured to only do a software scan once a day so all other scans will be hardware only which are fast scans and small in size. Are you seeing any issues on your server that warrant a change in how your machines are scanning? Backed up Inventory Scans in the LDSCAN folder?
As for Deep Freeze. You are definitely going to have to run full scans every time instead of Delta scans. Since the scan information is not being stored local, due to Deep Freeze, you are going to get a lot of Out of Sync errors. Another option is to customize a time when you can thaw your machines, run and Inventory Scan, and freeze them back. This will take a little more architecting, but it is an option.